CPSF4L

cleavage and polyadenylation specific factor 4 like

Basic information

Region (hg38): 17:73248448-73262352

Links

ENSG00000187959 ∙ NCBI:642843 ∙ ∙ HGNC:33632 ∙ Uniprot:A6NMK7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CPSF4L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPSF4L gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in CPSF4L

This is a list of pathogenic ClinVar variants found in the CPSF4L region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-73252639-T-G		not specified	Uncertain significance (May 17, 2023)
17-73252686-C-T		not specified	Uncertain significance (Jun 21, 2022)
17-73252693-C-T		not specified	Uncertain significance (May 11, 2022)
17-73252703-G-A		not specified	Uncertain significance (Dec 07, 2021)
17-73253974-C-G		not specified	Uncertain significance (Feb 05, 2024)
17-73254002-G-C		not specified	Uncertain significance (Nov 22, 2022)
17-73257770-C-T		not specified	Uncertain significance (Jul 19, 2022)
17-73257800-T-G		not specified	Uncertain significance (Dec 16, 2023)
17-73257822-G-C		not specified	Uncertain significance (May 01, 2024)
17-73260938-T-G		not specified	Uncertain significance (May 28, 2023)
17-73260957-A-C		not specified	Uncertain significance (Aug 30, 2022)
17-73260969-C-A		not specified	Uncertain significance (Aug 13, 2021)
17-73261745-G-T		not specified	Uncertain significance (Dec 01, 2022)
17-73261746-T-G		not specified	Uncertain significance (Oct 26, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPSF4L	protein_coding	protein_coding	ENST00000344935	6	13904

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00161	0.896	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.946	72	98.4	0.732	0.00000529	1186
Missense in Polyphen		20	28.969	0.69039		376
Synonymous	0.537	31	35.0	0.885	0.00000183	299
Loss of Function	1.42	6	11.1	0.540	6.43e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• pHI: 0.141
• ghis: 0.459

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.274

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cpsf4l

Gene ontology

• Biological process: pre-mRNA cleavage required for polyadenylation
• Cellular component: mRNA cleavage and polyadenylation specificity factor complex
• Molecular function: RNA binding;metal ion binding